tadded script for cyclic experiments on grendel - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
 (HTM) git clone git://src.adamsgaard.dk/sphere
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       ---
 (DIR) commit 8f29910a02f788f84cd8c28fe0d9024ec81d1203
 (DIR) parent d0149c57c01d10ebbe5943c6c9045fb71db3654d
 (HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
       Date:   Thu, 12 Mar 2015 15:46:35 +0100
       
       added script for cyclic experiments on grendel
       
       Diffstat:
         M python/halfshear-darcy-combined.py  |       2 +-
         A python/halfshear-per-cyclic.sh      |      50 +++++++++++++++++++++++++++++++
       
       2 files changed, 51 insertions(+), 1 deletion(-)
       ---
 (DIR) diff --git a/python/halfshear-darcy-combined.py b/python/halfshear-darcy-combined.py
       t@@ -141,7 +141,7 @@ t = t/t_DEM_to_t_real
        ## integrate velocities to displacement along x (xdispint)
        #  Taylor two term expansion
        xdispint  = numpy.zeros_like(t)
       -v_limit = 1.0e-7
       +v_limit = 1.0e-6
        dt  = (t[1] - t[0])
        dt2 = dt*2.
        for i in numpy.arange(t.size):
 (DIR) diff --git a/python/halfshear-per-cyclic.sh b/python/halfshear-per-cyclic.sh
       t@@ -0,0 +1,50 @@
       +#!/bin/sh
       +#PBS -N hs-per-cyc
       +#PBS -l nodes=1:ppn=3
       +#PBS -l walltime=48:00:00
       +#PBS -q qfermi
       +#PBS -M adc@geo.au.dk
       +#PBS -m abe
       +
       +# Grendel CUDA
       +source /com/gcc/4.6.4/load.sh
       +CUDAPATH=/com/cuda/5.5.22
       +export PATH=$HOME/bin:$PATH
       +export PATH=$CUDAPATH/bin:$PATH
       +export LD_LIBRARY_PATH=$CUDAPATH/lib64:$CUDAPATH/lib:$LD_LIBRARY_PATH
       +
       +# Manually installed Python modules
       +export PYTHONPATH=$HOME/.local/lib/python:$PYTHONPATH
       +export PYTHONPATH=$HOME/.local/lib64/python:$PYTHONPATH
       +
       +# Manually installed Python
       +#export PATH=/home/adc/.local/bin:$PATH
       +
       +# Shared Python2.7
       +PYTHON=/com/python/2.7.6
       +export PYTHONPATH=$PYTHON/lib:$PYTHONPATH
       +export PATH=$PYTHON/bin:$PATH
       +
       +echo "`whoami`@`hostname`"
       +echo "Start at `date`"
       +
       +ORIGDIR=/home/adc/code/sphere
       +#WORKDIR=/scratch/$PBS_JOBID
       +WORKDIR=$ORIGDIR
       +
       +#cp -r $ORIGDIR/* $WORKDIR
       +
       +cd $WORKDIR
       +nvidia-smi
       +rm CMakeCache.txt
       +cmake . && make
       +cd python
       +# $ ipython halfshear-darcy-stress-starter.py <device> <fluid> <c_phi> <k_c> <sigma_0> <mu> <shear_stress>
       +python halfshear-darcy-stress-mod-starter.py 0 1 1.0 3.5e-13 80000.0 1.040e-7 10000.0 60000.0 0.2 1.0 &
       +python halfshear-darcy-stress-mod-starter.py 1 1 1.0 3.5e-13 80000.0 1.040e-7 10000.0 62500.0 0.2 1.0 &
       +python halfshear-darcy-stress-mod-starter.py 2 1 1.0 3.5e-13 80000.0 1.040e-7 10000.0 65000.0 0.2 1.0 &
       +wait
       +
       +#cp $WORKDIR/output/* $ORIGDIR/output/
       +
       +echo "End at `date`"